The present invention provides a method and a composition for detecting the levels of a plurality of biomolecular probes in a sample.
DNA-based arrays can provide a simple way to explore the expression of a single polymorphic gene or a large number of genes. When the expression of a single gene is explored, DNA-based arrays are employed to detect the expression of specific gene variants. For example, a p53 gene array is used to determine whether individuals are carrying mutations that predispose them to cancer. Alternatively, a P450 gene array is used to determine whether individuals have one of a number of specific mutations that could result in increased drug metabolism, drug resistance or drug toxicity.
DNA-based array technology is especially relevant to the rapid screening of expression of a large number of genes. There is a growing awareness that gene expression is affected in a global fashion. A genetic predisposition, disease or therapeutic treatment may affect, directly or indirectly, the expression of a large number of genes. In some cases a relationship between a disease or therapeutic treatment and the expression of particular genes may be expected, such as where the genes are known to be part of a signaling pathway implicated in a disease. In other cases, such as when the genes"" function is unidentified or the genes participate in separate signaling pathways, the relationship between a disease and particular genes may be unexpected. Therefore, DNA-based arrays can be used to investigate how genetic predisposition, disease, or therapeutic treatment may affect the expression of individual genes or a group of genes.
The present invention provides a hybridization composition for detecting the levels of a plurality of biomolecular probes in a sample. The composition comprises (a) a capillary-like casing; and (b) a substrate immobilized in said casing. The substrate""s surface contains a plurality of regions arranged in a defined manner with respect to the length of said casing and each of the regions has one or more different immobilized target. Additionally, the substrate""s surface is in close proximity with the inner surface of said casing so as to minimize the ratio of liquid volume contained within said casing to the substrate""s surface area. The linear density of the plurality of defined regions is greater than 1/cm, preferably is greater than 1xc3x97103/cm, and more preferably is greater than 1xc3x97106/cm.
In one preferred embodiment, the biomolecular probes comprise polynucleotide probes in a sample and the targets are complementary polynucleotide sequences. In another preferred embodiment, the ratio of liquid volume contained within said casing to hybridization surface area is less than about 1xc3x9710xe2x88x925 m, preferably less than 1xc3x9710xe2x88x927 m, more preferably less than 1xc3x9710xe2x88x929 m. In yet another preferred embodiment, the substrate is a plurality of beads whose diameters approximate the inner diameter of the capillary-like casing. In a another preferred embodiment, the substrate is a rod whose diameter approximates the inner diameter of the capillary-like casing. Typically, the diameter of the substrate is more than 90%, preferably more than 95%, of the inner diameter of the capillary-like casing. In a further embodiment, the substrate is an agarose plug flush against the inner surface of the capillary-like casing.
The present invention also provides a method for detecting the levels of a plurality of biomolecular probes in a sample. The method comprises (i) contacting the sample comprising the plurality of biomolecular probes with a hybridization composition comprising (a) a capillary-like casing and (b) a substrate immobilized in said casing under conditions effective to form hybridization complexes between biomolecular probes and immobilized targets; and (ii) detecting the hybridization complexes.